Add nf-core pipelines containers create-configs

CHANGELOG.md

@@ -1,5 +1,11 @@
 # nf-core/tools: Changelog
 
+## v4.2.0dev
+
+### General
+
+- Add `nf-core pipelines containers create-configs` to regenerate the pipeline `conf/containers_*.config` files ([#XXXX](https://github.com/nf-core/tools/pull/XXXX))
+
 ## [v4.1.0 - Marshalled Mamba](https://github.com/nf-core/tools/releases/tag/4.1.0) - [2026-07-29]
 
 ### General

nf_core/__main__.py

@@ -167,7 +167,8 @@ def interface(ctx):
 @nf_core_cli.group(aliases=["p", "pipeline"])
 @click.command_panel("For users", commands=["download", "create-params-file", "launch", "list"])
 @click.command_panel(
-    "For developers", commands=["bump-version", "create", "create-logo", "lint", "rocrate", "schema", "sync"]
+    "For developers",
+    commands=["bump-version", "containers", "create", "create-logo", "lint", "rocrate", "schema", "sync"],
 )
 @click.pass_context
 def pipelines(ctx):
@@ -209,6 +210,36 @@ def command_pipelines_create(ctx, name, description, author, version, force, out
     pipelines_create(ctx, name, description, author, version, force, outdir, template_yaml, organisation)
 
 
+# nf-core pipelines containers subcommands
+@pipelines.group("containers", aliases=["container"])
+@click.pass_context
+def pipelines_containers(ctx):
+    """
+    Commands to manage pipeline containers.
+    """
+    ctx.ensure_object(dict)
+
+
+# nf-core pipelines containers create-configs
+@pipelines_containers.command("create-configs")
+@click.option(
+    "-d",
+    "--dir",
+    "directory",
+    type=click.Path(exists=True),
+    default=".",
+    help=r"Pipeline directory [dim]\[default: current working directory][/]",
+)
+@click.pass_context
+def command_pipelines_containers_create_configs(ctx, directory):
+    """
+    Regenerate the pipeline container config files.
+    """
+    from nf_core.commands_pipelines import pipelines_containers_create_configs
+
+    pipelines_containers_create_configs(ctx, directory)
+
+
 # nf-core pipelines lint
 @pipelines.command("lint", aliases=["l"])
 @click.option(

nf_core/commands_pipelines.py

@@ -99,6 +99,29 @@ def pipelines_bump_version(ctx, new_version, directory, nextflow):
         sys.exit(1)
 
 
+# nf-core pipelines containers create-configs
+def pipelines_containers_create_configs(ctx, directory):
+    """
+    Regenerate the pipeline container config files.
+
+    Scans all modules installed in the pipeline and rewrites the
+    `conf/containers_*.config` files from their `meta.yml` container entries.
+
+    Useful after resolving a template sync merge conflict in these files: the
+    contents are always regenerated from scratch, so whatever they contained
+    before is discarded.
+    """
+    from nf_core.pipelines.containers_utils import ContainerConfigs
+    from nf_core.utils import is_pipeline_directory
+
+    try:
+        is_pipeline_directory(directory)
+        ContainerConfigs(Path(directory)).generate_container_configs()
+    except UserWarning as e:
+        log.error(e)
+        sys.exit(1)
+
+
 # nf-core pipelines lint
 def pipelines_lint(
     ctx,

tests/pipelines/test_container_configs.py

@@ -2,8 +2,10 @@
 
 import shutil
 
+import pytest
 import ruamel.yaml
 
+from nf_core.commands_pipelines import pipelines_containers_create_configs
 from nf_core.modules.install import ModuleInstall
 from nf_core.pipelines.containers_utils import PLATFORMS, ContainerConfigs
 
@@ -99,3 +101,22 @@ def test_generate_container_configs_skips_meta_without_containers(self) -> None:
             cfg_path = conf_dir / f"containers_{p_name}.config"
             if cfg_path.exists():
                 assert "FAKE" not in cfg_path.read_text(), f"{cfg_path.name} contains entry for FAKE module"
+
+
+class TestPipelinesContainersCommand(TestPipelines):
+    """Tests for the ``nf-core pipelines containers`` command function."""
+
+    def test_regenerates_config_files(self) -> None:
+        """Existing config file contents are replaced."""
+        cfg_path = self.pipeline_dir / "conf" / "containers_docker_amd64.config"
+        original = cfg_path.read_text()
+        cfg_path.write_text("not a container config\n")
+
+        pipelines_containers_create_configs(None, str(self.pipeline_dir))
+
+        assert cfg_path.read_text() == original
+
+    def test_exits_when_not_a_pipeline(self) -> None:
+        """A directory without main.nf exits with an error."""
+        with pytest.raises(SystemExit):
+            pipelines_containers_create_configs(None, str(self.tmp_dir))